0800-appendix-058159.Rmd

```{r setup-58159, eval = F}
knitr::opts_chunk$set(echo=FALSE, message=FALSE, warning=FALSE)
source('R/packages.R')
source('R/functions.R')
source('R/functions-phase2.R')
source('R/tables-phase2.R')
source('R/tables.R')
source('R/extract-fish.R')
source('R/functions-fish.R')


```



```{r  load-data-58159}
my_site <- 58159
my_site2 <- 58158

```

`r appendix_title()`

## Site Location {-}

PSCIS crossing `r as.character(my_site)` is located on `r my_pscis_info() %>% pull(stream_name)` on the `r my_overview_info() %>% pull(road_name)` accessed from Highway 16 immediately south of Telkwa, BC. The `r my_overview_info() %>% pull(road_name)` is a private road owned by the Woodmere Nursery.  At the time of field surveys it was used to access a newly constructed agricultural facility and by nursery operations to access a waste storage/burn pile area.

```{r eval=F}
##idon't think we need this here but...
#During 2020 surveys, PSCIS culvert 197669 was documented on `r my_pscis_info() %>% pull(stream_name)`, 1.2km upstream of the FSR.

```

<br>

## Background {-}


`r my_pscis_info() %>% pull(stream_name)` drains McDowell Lake (35ha), Dorsay Lake (4ha) and one other unnamed lake (9ha) flowing from McDowell Lake in a south then west direction for approximately 9km to the confluence with the Bulkley River. At crossing `r as.character(my_site)`, `r my_pscis_info() %>% pull(stream_name)` is a `r my_bcfishpass() %>% pull(stream_order) %>% english::ordinal()` order stream with a watershed area upstream of the crossing of approximately `r round(my_bcfishpass() %>% pull(watershed_upstr_ha)/100,1)`km^2^. The elevation of the watershed ranges from a maximum of 1000 to 520m at PSCIS crossing `r as.character(my_site)`. `r my_pscis_info() %>% pull(stream_name)` is known to contain coho and rainbow trout upstream of the subject culvert [@data_fish_obs]. There are numerous stream crossing structures located on `r my_pscis_info() %>% pull(stream_name)` upstream of `r as.character(my_site)` including crossings on Highway 16, an unnamed road 300m upstream of the highway, Woodmere Road and others.

<br>


PSCIS stream crossings `r as.character(my_site)` and `r as.character(my_site2)` were rated as high priorities for follow up by both @irvine2018AnalysisPriority and @smith2018AssessingBarriers due to significant quantities of upstream habitat suitable for salmonid rearing. A map of the watershed is provided in map attachment [`r my_bcfishpass() %>% pull(dbm_mof_50k_grid)`](`r my_mapsheet()`).

<br>

## Stream Characteristics at Crossing {-}

At the time of the survey, the culvert was un-embedded, non-backwatered and considered a barrier to upstream fish passage. The pipe was `r my_pscis_info() %>% pull(diameter_or_span_meters)`m in diameter with a pipe length of `r my_pscis_info() %>% pull(length_or_width_meters)`m, a culvert slope of `r my_pscis_info() %>% pull(culvert_slope_percent)`%, a stream width ratio of `r my_pscis_info() %>% pull(stream_width_ratio)` and an outlet drop of `r my_pscis_info() %>% pull(outlet_drop_meters)`m (Table \@ref(tab:tab-culvert-58159)). Water temperature was `r my_habitat_info() %>% filter(rowname == 'temperature c') %>% pull(us)`$^\circ$C, pH was `r my_habitat_info() %>% filter(rowname == 'p h') %>% pull(us)` and conductivity was `r my_habitat_info() %>% filter(rowname == 'conductivity m s cm') %>% pull(us)`uS/cm.  


<br>

```{r eval=F}
##this is useful to get some comments for the report
hab_site %>% filter(site == my_site & location == 'us') %>% pull(comments)
my_priority <-  my_priority_info()

```

## Stream Characteristics Downstream {-}

The stream was surveyed downstream from the culvert for `r my_priority_info(loc = 'ds') %>% pull(survey_length_m)`m `r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-58159-01) - \\@ref(fig:photo-58159-02))")}else(knitr::asis_output("(Figure \\@ref(fig:photo-58159-d01))"))`. Overall, total cover amount was rated as `r my_habitat_info2(loc = 'ds') %>% filter(rowname == 'total cover') %>% pull(v)` with  `r my_habitat_info2(loc = 'ds') %>% filter(v == 'dominant') %>% pull(rowname)` dominant. Cover was also present as `r my_habitat_info2(loc = 'ds') %>% filter(v == 'sub-dominant') %>% pull(rowname) %>% knitr::combine_words()` (Table \@ref(tab:tab-habitat-summary-58159)). The average channel width was `r my_habitat_info3(loc = 'ds', row = 'avg channel width m')`m, the average wetted width was `r my_habitat_info3(loc = 'ds', row = 'avg wetted width m')`m and the average gradient was `r my_habitat_info3(loc = 'ds', row = 'average gradient percent')`%. The dominant substrate was `r my_habitat_info3(loc = 'ds', row = "bed material dominant")` with `r my_habitat_info3(loc = 'ds', row = "bed material subdominant")` subdominant. Habitat was rated as `r my_priority_info(loc = 'ds') %>%  pull(hab_value)` as it was considered an important migration corridor with moderate value habitat for fry/juvenile salmonid rearing.  

<br>

## Stream Characteristics Upstream {-}

The stream was surveyed upstream from `r as.character(my_site)` for `r my_priority_info(loc = 'us') %>% pull(survey_length_m)`m `r if(gitbook_on){knitr::asis_output("(Figures \\@ref(fig:photo-58159-03) - \\@ref(fig:photo-58159-04))")} else(knitr::asis_output("(Figure \\@ref(fig:photo-58159-d02))"))`. Within the area surveyed, total cover amount was rated as `r my_habitat_info2(loc = 'us') %>% filter(rowname == 'total cover') %>% pull(v)` with  `r my_habitat_info2(loc = 'us') %>% filter(v == 'dominant') %>% pull(rowname)` dominant. Cover was also present as `r my_habitat_info2(loc = 'us') %>% filter(v == 'sub-dominant') %>% pull(rowname) %>% knitr::combine_words()` (Table \@ref(tab:tab-habitat-summary-58159)). The average channel width was `r my_habitat_info3(loc = 'us', row = 'avg channel width m')`m, the average wetted width was `r my_habitat_info3(loc = 'us', row = 'avg wetted width m')`m and the average gradient was `r my_habitat_info3(loc = 'us', row = 'average gradient percent')`%.  Habitat value was rated as `r my_priority_info(loc = 'us') %>% pull(hab_value)` for salmonid rearing and spawning. 


<br>

PSCIS culvert `r as.character(my_site2)` was documented on `r my_pscis_info() %>% pull(stream_name)`, 500m upstream on Highway 16. At the time of the survey the culvert had been newly replaced with a baffled structure embedded with a natural cobble and gravel substrates.  Although ranked as a barrier to upstream fish passage using the provincial metric the crossing is likely not a barrier during most flows for adult anadromous salmon and fluvial salmonids migrating upstream from the Bulkley River. The pipe was `r my_pscis_info(dat = pscis_all, site = my_site2) %>% pull(diameter_or_span_meters)`m in diameter with a pipe length of `r my_pscis_info(dat = pscis_all, site = my_site2) %>% pull(length_or_width_meters)`m, a culvert slope of `r my_pscis_info(dat = pscis_all, site = my_site2) %>% pull(culvert_slope_percent)`%, a stream width ratio of `r my_pscis_info(dat = pscis_all, site = my_site2) %>% pull(stream_width_ratio)` and an outlet drop of `r my_pscis_info(dat = pscis_all, site = my_site2) %>% pull(outlet_drop_meters)`m (Table \@ref(tab:tab-culvert-58158)).

<br>

[PSCIS crossing 123544](http://a100.gov.bc.ca/pub/pscismap/imageViewer.do?assessmentId=123724), located on an unnamed road approximately 300m upstream of Highway 16 has been documented as a barrier in the PSCIS system.  The culvert is documented as 30m long, with a 1m diameter, a slope of 3.5% and an outlet drop of 0.3m. The culvert is noted as not embedded and not backwatered.

<br>


Table \@ref(tab:tab-culvert-bcfp-58159) `r text_ref_tab_summary_bcfp()` 

<br>

## Fish Sampling {-}

To assess potential impacts of the culvert on fisheries values in the stream, electrofishing was conducted upstream and downstream of the crossing.  A total of `r tab_fish_summary %>% filter(site_id == paste0(my_site, '_ds') & species_code == 'CO') %>% pull(count_fish)` coho were captured downstream with `r tab_fish_summary %>% filter(site_id == paste0(my_site, '_us') & species_code == 'CO') %>% pull(count_fish)` coho captured upstream. Although there is only moderate confidence in their identification, `r tab_fish_summary %>% filter(site_id == paste0(my_site, '_ds') & species_code == 'CH') %>% pull(count_fish)` fish captured were identified as chinook.  With the exception of one coho, only rainbow trout (`r tab_fish_summary %>% filter(site_id == paste0(my_site, '_us') & species_code == 'RB') %>% pull(count_fish)` fish) were captured upstream. Sampling results are summarized in Tables \@ref(tab:tab-fish-site-58159) - \@ref(tab:tab-fish-dens-58159) and Figure \@ref(fig:plot-fish-box-58159).


<br>

## Structure Remediation and Cost Estimate {-}

Structure replacement with a bridge (`r my_pscis_info() %>% pull(recommended_diameter_or_span_meters)`m span) is recommended to provide access to the habitat located upstream of PSCIS crossing `r as.character(my_site)`. The cost of the work is estimated at \$`r format(my_cost_estimate() %>% pull(cost_est_1000s) * 1000, big.mark = ',')` for a cost benefit of `r as.character(my_cost_estimate() %>% pull(cost_net))` linear m/\$1000 and `r as.character(my_cost_estimate() %>% pull(cost_area_net))`m^2^/\$1000.


<br>


## Conclusion {-}

There is `r my_priority_info() %>% pull(upstream_habitat_length_km)`km of habitat upstream of crossing `r as.character(my_site)` to PSCIS crossing 123544 located on an unnamed road approximately 300m upstream of Highway 16.  Habitat in this area was rated as `r my_priority_info(sit = my_site, loc = 'us') %>% pull(hab_value)` value for salmonid rearing/spawning.  `r my_overview_info() %>% pull(road_name)` is on private land owned by the Woodmere Nursury.  The crossing was ranked as a `r my_priority_info() %>% pull(priority)` priority for proceeding to design for replacement. Although remediation of fish passage at `r as.character(my_site)` is considered beneficial, detailed habitat confirmation assessments of upstream culverts (PSCIS 123544) could be pursued to scope for additional potential habitat gains possible within the same system.

<br>

```{r tab-culvert-58159, eval = T}
print_tab_summary()

```


<br>


```{r tab-culvert-58158, eval = T}
print_tab_summary(site = my_site2, dat = pscis_reassessments, site_photo_id = my_site2)

```


<br>

```{r tab-habitat-summary-58159}
tab_hab_summary %>% 
  filter(Site  == my_site) %>% 
  # select(-Site) %>% 
  my_kable(caption_text = paste0('Summary of habitat details for PSCIS crossing ', my_site, '.'))

```

<br>

```{r tab-culvert-bcfp-58159, eval = T}
print_tab_summary_bcfp()
```


<br>

```{r tab-fish-site-58159, eval=T}
my_caption <- paste0('Electrofishing sites for PSCIS crossing ', my_site, '.')

tab_fish_site() %>% 
  my_kable(caption_text = my_caption)
```


<br>

```{r tab-fish-dens-58159, eval=T}
my_caption <- paste0('Fish densities (fish/100m2) for PSCIS crossing ', my_site, '.')

tab_fish_dens() %>% 
  my_kable(caption_text = my_caption)
```

<br>

```{r plot-fish-box-58159, fig.cap= my_caption, eval=T}
my_caption <- paste0('Densities of fish captured (fish/100m2) during electrofishing upstream and downstream of PSCIS crossing ', my_site, '.')

plot_fish_box() 

```


<br>


```{r photo-58159-01-prep, eval=T}
my_photo1 = pull_photo_by_str(str_to_pull = '_d1_')

my_caption1 = paste0('Typical habitat downstream of PSCIS crossing ', my_site, '.')

```

```{r photo-58159-01, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo1))
```

<br>

```{r photo-58159-02-prep}
my_photo2 = pull_photo_by_str(str_to_pull = '_df1_')

my_caption2 = paste0('Chinook captured downstream of PSCIS crossing ', my_site, '.')
```

```{r photo-58159-02, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo2))

```

<br>

```{r photo-58159-d01, fig.cap = my_caption, fig.show="hold", out.width= c("49.5%","1%","49.5%"), eval=identical(gitbook_on, FALSE)}
##we could put 2 photos in on box but it is lots of extra work with the crossreferences. pdfs suck anyway.  Don't get too custom with it!!!

# my_photo1 = pull_photo_by_str(str_to_pull = '_d1_')
# my_caption1 = paste0('Typical habitat downstream of PSCIS crossing ', my_site, '.')
# 
# my_photo2 = pull_photo_by_str(str_to_pull = '_u1_')
# my_caption2 = paste0('Typical habitat upstream of PSCIS crossing ', my_site, '.')

my_caption <- paste0('Left: ', my_caption1, ' Right: ', my_caption2)

knitr::include_graphics(get_img_path(photo = my_photo1))
knitr::include_graphics("fig/pixel.png")
knitr::include_graphics(get_img_path(photo = my_photo2))
```


```{r photo-58159-03-prep}
my_photo1 = pull_photo_by_str(str_to_pull = '_u1_')

my_caption1 = paste0('Typical habitat upstream of PSCIS crossing ', my_site, '.')

```

```{r photo-58159-03, fig.cap= my_caption1, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo1))

```

<br>

```{r photo-58159-04-prep}
my_photo2 = pull_photo_by_str(str_to_pull = '_uf1_')

my_caption2 = paste0('Coho captured upstream of PSCIS crossing ', my_site, '.')

```

```{r photo-58159-04, fig.cap= my_caption2, out.width = photo_width, eval=gitbook_on}
grid::grid.raster(get_img(photo = my_photo2))
```

```{r photo-58159-d02, fig.cap = my_caption, fig.show="hold", out.width= c("49.5%","1%","49.5%"), eval=identical(gitbook_on, FALSE)}

my_caption <- paste0('Left: ', my_caption1, ' Right: ', my_caption2)

knitr::include_graphics(get_img_path(photo = my_photo1))
knitr::include_graphics("fig/pixel.png")
knitr::include_graphics(get_img_path(photo = my_photo2))
```